There are other differences, but they are internal, like armor for the flight deck and magazines.

Here is "the class," and there is a description near the top you can read:

https://www.seaforces.org/usnships/cvn/Nimitz-class.htm

There is also an overhead view of both Lincoln and Bush. You can see the flight deck shape is not changed.

I would note that the Trumpeter Nimitz kits all came from inaccurate Russian drawings, and their elevator shapes are slightly off, making the kit flight deck not accurate to begin with. However, in this case, if this inaccuracy does not bother you for the intended kit, it need not bother you for the conversion. The "class is the class."